Starting phenix.real_space_refine on Fri Sep 11 19:03:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7c7q_30300/09_2026/7c7q_30300.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c7q_30300/09_2026/7c7q_30300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7c7q_30300/09_2026/7c7q_30300.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7c7q_30300/09_2026/7c7q_30300.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7c7q_30300/09_2026/7c7q_30300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c7q_30300/09_2026/7c7q_30300.map" model { file = "/net/cci-nas-00/data/ceres_data/7c7q_30300/09_2026/7c7q_30300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c7q_30300/09_2026/7c7q_30300.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 61 5.16 5 Cl 1 4.86 5 C 7057 2.51 5 N 1789 2.21 5 O 1983 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10894 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5406 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 28, 'TRANS': 649} Chain breaks: 2 Chain: "B" Number of atoms: 5339 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 670, 5328 Classifications: {'peptide': 670} Link IDs: {'PTRANS': 27, 'TRANS': 642} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 670, 5328 Classifications: {'peptide': 670} Link IDs: {'PTRANS': 27, 'TRANS': 642} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 5433 Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 107 Unusual residues: {'2C0': 1, 'FN0': 1, 'NAG': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE B 572 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 572 " occ=0.50 Time building chain proxies: 3.01, per 1000 atoms: 0.28 Number of scatterers: 10894 At special positions: 0 Unit cell: (78.078, 100.386, 165.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 61 16.00 F 3 9.00 O 1983 8.00 N 1789 7.00 C 7057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 246 " distance=2.04 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 663 " - pdb=" SG CYS A 761 " distance=1.88 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 648 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM10799 O5 NAG A1004 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 409 " " NAG A1002 " - " ASN A 440 " " NAG A1003 " - " ASN A 482 " " NAG A1004 " - " ASN A 502 " " NAG A1005 " - " ASN A 514 " " NAG B1001 " - " ASN B 389 " " NAG B1002 " - " ASN B 404 " " NAG B1003 " - " ASN B 453 " Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 616.6 milliseconds 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2524 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 56.2% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 184 through 202 Proline residue: A 190 - end of helix removed outlier: 3.877A pdb=" N GLU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 234 removed outlier: 3.666A pdb=" N LYS A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 271 through 276 removed outlier: 4.145A pdb=" N ASN A 276 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 292 through 304 removed outlier: 4.297A pdb=" N THR A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 334 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 367 through 382 removed outlier: 4.092A pdb=" N LYS A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 419 removed outlier: 4.154A pdb=" N GLU A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 454 Processing helix chain 'A' and resid 457 through 461 Processing helix chain 'A' and resid 466 through 484 removed outlier: 3.519A pdb=" N ALA A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 515 removed outlier: 3.729A pdb=" N SER A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 616 Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 626 through 643 removed outlier: 3.567A pdb=" N ASN A 630 " --> pdb=" O GLN A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 649 removed outlier: 3.835A pdb=" N LEU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 679 removed outlier: 3.755A pdb=" N CYS A 663 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN A 664 " --> pdb=" O PRO A 660 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 708 through 732 removed outlier: 3.949A pdb=" N VAL A 714 " --> pdb=" O LEU A 710 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 791 Processing helix chain 'A' and resid 801 through 826 Proline residue: A 821 - end of helix removed outlier: 3.604A pdb=" N MET A 824 " --> pdb=" O ALA A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 861 removed outlier: 3.884A pdb=" N ALA A 840 " --> pdb=" O PHE A 836 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 844 " --> pdb=" O ALA A 840 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) Proline residue: A 855 - end of helix Processing helix chain 'B' and resid 70 through 92 removed outlier: 4.022A pdb=" N GLY B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) Proline residue: B 79 - end of helix removed outlier: 3.703A pdb=" N LEU B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 124 removed outlier: 3.783A pdb=" N LEU B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 145 removed outlier: 3.671A pdb=" N ILE B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER B 145 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 149 Processing helix chain 'B' and resid 160 through 165 removed outlier: 3.539A pdb=" N LEU B 163 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP B 165 " --> pdb=" O VAL B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 181 Processing helix chain 'B' and resid 182 through 192 Processing helix chain 'B' and resid 205 through 219 removed outlier: 3.631A pdb=" N GLY B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 246 Processing helix chain 'B' and resid 256 through 268 removed outlier: 3.933A pdb=" N ALA B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 292 removed outlier: 3.562A pdb=" N GLN B 292 " --> pdb=" O TRP B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 312 Processing helix chain 'B' and resid 334 through 346 Processing helix chain 'B' and resid 354 through 376 removed outlier: 3.506A pdb=" N LEU B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 405 removed outlier: 3.680A pdb=" N GLU B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 506 removed outlier: 3.664A pdb=" N LEU B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 514 Processing helix chain 'B' and resid 516 through 532 removed outlier: 3.694A pdb=" N ILE B 523 " --> pdb=" O MET B 519 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 538 removed outlier: 3.629A pdb=" N LEU B 536 " --> pdb=" O SER B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 583 removed outlier: 3.997A pdb=" N THR B 554 " --> pdb=" O GLU B 550 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR B 557 " --> pdb=" O CYS B 553 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET B 571 " --> pdb=" O ALA B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 619 removed outlier: 3.921A pdb=" N ILE B 600 " --> pdb=" O LYS B 596 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL B 601 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 618 " --> pdb=" O CYS B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 680 removed outlier: 4.250A pdb=" N TRP B 656 " --> pdb=" O HIS B 652 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 674 " --> pdb=" O PHE B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 711 removed outlier: 3.729A pdb=" N ILE B 704 " --> pdb=" O GLY B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 748 removed outlier: 3.536A pdb=" N LEU B 726 " --> pdb=" O CYS B 722 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 728 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 736 " --> pdb=" O SER B 732 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL B 739 " --> pdb=" O THR B 735 " (cutoff:3.500A) Proline residue: B 742 - end of helix removed outlier: 3.853A pdb=" N THR B 746 " --> pdb=" O PRO B 742 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 216 removed outlier: 8.177A pdb=" N ILE A 240 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N TYR A 171 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU A 242 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY A 173 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU A 175 " --> pdb=" O PRO A 244 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE A 240 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N LEU A 265 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU A 242 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 336 through 343 removed outlier: 6.918A pdb=" N ILE A 309 " --> pdb=" O PHE A 339 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLN A 341 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR A 311 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N PHE A 343 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN A 313 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE A 361 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE A 393 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A 425 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN A 541 " --> pdb=" O LYS A 549 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LYS A 549 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 517 through 520 Processing sheet with id=AA4, first strand: chain 'A' and resid 580 through 584 removed outlier: 5.922A pdb=" N ILE A 581 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLN A 757 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N THR A 583 " --> pdb=" O GLN A 757 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLU A 759 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 105 removed outlier: 5.847A pdb=" N LEU B 56 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ARG B 102 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE B 58 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N TYR B 104 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY B 60 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 9.905A pdb=" N MET B 129 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N SER B 57 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N PHE B 131 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N MET B 59 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL B 152 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 225 through 232 removed outlier: 7.719A pdb=" N THR B 200 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N THR B 229 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N THR B 202 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER B 231 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE B 250 " --> pdb=" O ARG B 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 315 through 319 removed outlier: 6.436A pdb=" N ILE B 426 " --> pdb=" O GLU B 441 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLU B 441 " --> pdb=" O ILE B 426 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N PHE B 428 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 435 " --> pdb=" O GLN B 432 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 407 through 410 Processing sheet with id=AA9, first strand: chain 'B' and resid 470 through 474 removed outlier: 6.127A pdb=" N LEU B 471 " --> pdb=" O ARG B 642 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU B 644 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLN B 473 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLU B 646 " --> pdb=" O GLN B 473 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1681 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.46 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2454 1.33 - 1.45: 2440 1.45 - 1.57: 6158 1.57 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 11150 Sorted by residual: bond pdb=" C13 FN0 A1006 " pdb=" O3 FN0 A1006 " ideal model delta sigma weight residual 1.190 1.259 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C17 FN0 A1006 " pdb=" F1 FN0 A1006 " ideal model delta sigma weight residual 1.336 1.290 0.046 2.00e-02 2.50e+03 5.38e+00 bond pdb=" C SER B 533 " pdb=" O SER B 533 " ideal model delta sigma weight residual 1.236 1.210 0.026 1.29e-02 6.01e+03 3.96e+00 bond pdb=" CA ASN A 409 " pdb=" C ASN A 409 " ideal model delta sigma weight residual 1.524 1.547 -0.023 1.29e-02 6.01e+03 3.29e+00 bond pdb=" CA ALA B 532 " pdb=" C ALA B 532 " ideal model delta sigma weight residual 1.522 1.498 0.024 1.41e-02 5.03e+03 2.90e+00 ... (remaining 11145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 14986 2.77 - 5.55: 132 5.55 - 8.32: 11 8.32 - 11.10: 3 11.10 - 13.87: 1 Bond angle restraints: 15133 Sorted by residual: angle pdb=" N THR B 238 " pdb=" CA THR B 238 " pdb=" C THR B 238 " ideal model delta sigma weight residual 113.38 99.51 13.87 1.23e+00 6.61e-01 1.27e+02 angle pdb=" N ASN A 409 " pdb=" CA ASN A 409 " pdb=" C ASN A 409 " ideal model delta sigma weight residual 111.36 121.71 -10.35 1.09e+00 8.42e-01 9.02e+01 angle pdb=" C ILE B 534 " pdb=" CA ILE B 534 " pdb=" CB ILE B 534 " ideal model delta sigma weight residual 112.14 106.19 5.95 1.35e+00 5.49e-01 1.94e+01 angle pdb=" N ASP B 454 " pdb=" CA ASP B 454 " pdb=" CB ASP B 454 " ideal model delta sigma weight residual 114.17 109.36 4.81 1.14e+00 7.69e-01 1.78e+01 angle pdb=" N GLN A 503 " pdb=" CA GLN A 503 " pdb=" C GLN A 503 " ideal model delta sigma weight residual 113.17 118.06 -4.89 1.26e+00 6.30e-01 1.50e+01 ... (remaining 15128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 6109 17.37 - 34.75: 372 34.75 - 52.12: 83 52.12 - 69.49: 9 69.49 - 86.86: 4 Dihedral angle restraints: 6577 sinusoidal: 2655 harmonic: 3922 Sorted by residual: dihedral pdb=" CB CYS B 553 " pdb=" SG CYS B 553 " pdb=" SG CYS B 648 " pdb=" CB CYS B 648 " ideal model delta sinusoidal sigma weight residual 93.00 166.99 -73.99 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CB CYS A 663 " pdb=" SG CYS A 663 " pdb=" SG CYS A 761 " pdb=" CB CYS A 761 " ideal model delta sinusoidal sigma weight residual -86.00 -25.51 -60.49 1 1.00e+01 1.00e-02 4.87e+01 dihedral pdb=" CB CYS B 237 " pdb=" SG CYS B 237 " pdb=" SG CYS B 266 " pdb=" CB CYS B 266 " ideal model delta sinusoidal sigma weight residual -86.00 -29.81 -56.19 1 1.00e+01 1.00e-02 4.26e+01 ... (remaining 6574 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.255: 1719 0.255 - 0.510: 6 0.510 - 0.765: 0 0.765 - 1.019: 1 1.019 - 1.274: 2 Chirality restraints: 1728 Sorted by residual: chirality pdb=" C1 NAG A1005 " pdb=" ND2 ASN A 514 " pdb=" C2 NAG A1005 " pdb=" O5 NAG A1005 " both_signs ideal model delta sigma weight residual False -2.40 -1.13 -1.27 2.00e-01 2.50e+01 4.06e+01 chirality pdb=" C1 NAG B1003 " pdb=" ND2 ASN B 453 " pdb=" C2 NAG B1003 " pdb=" O5 NAG B1003 " both_signs ideal model delta sigma weight residual False -2.40 -1.35 -1.05 2.00e-01 2.50e+01 2.74e+01 chirality pdb=" C1 NAG B1002 " pdb=" ND2 ASN B 404 " pdb=" C2 NAG B1002 " pdb=" O5 NAG B1002 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.18e+01 ... (remaining 1725 not shown) Planarity restraints: 1887 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 502 " -0.028 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" CG ASN A 502 " 0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN A 502 " -0.212 2.00e-02 2.50e+03 pdb=" ND2 ASN A 502 " 0.494 2.00e-02 2.50e+03 pdb=" C1 NAG A1004 " -0.333 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1001 " -0.305 2.00e-02 2.50e+03 2.57e-01 8.28e+02 pdb=" C7 NAG A1001 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A1001 " -0.187 2.00e-02 2.50e+03 pdb=" N2 NAG A1001 " 0.443 2.00e-02 2.50e+03 pdb=" O7 NAG A1001 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 409 " 0.208 2.00e-02 2.50e+03 2.56e-01 8.17e+02 pdb=" CG ASN A 409 " -0.086 2.00e-02 2.50e+03 pdb=" OD1 ASN A 409 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN A 409 " -0.420 2.00e-02 2.50e+03 pdb=" C1 NAG A1001 " 0.315 2.00e-02 2.50e+03 ... (remaining 1884 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 204 2.69 - 3.25: 10829 3.25 - 3.80: 16747 3.80 - 4.35: 22187 4.35 - 4.90: 36780 Nonbonded interactions: 86747 Sorted by model distance: nonbonded pdb=" O3 NAG A1003 " pdb=" O7 NAG A1003 " model vdw 2.144 3.040 nonbonded pdb=" O PHE A 366 " pdb=" OH TYR A 396 " model vdw 2.178 3.040 nonbonded pdb=" CG ASN A 502 " pdb=" O5 NAG A1004 " model vdw 2.205 2.616 nonbonded pdb=" OD2 ASP B 360 " pdb=" OG1 THR B 412 " model vdw 2.217 3.040 nonbonded pdb=" O ASN A 409 " pdb=" OD1 ASN A 409 " model vdw 2.220 3.040 ... (remaining 86742 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.080 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 11165 Z= 0.209 Angle : 1.077 42.386 15171 Z= 0.514 Chirality : 0.068 1.274 1728 Planarity : 0.009 0.257 1879 Dihedral : 11.700 86.863 4032 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.20), residues: 1337 helix: -1.57 (0.17), residues: 696 sheet: -1.85 (0.31), residues: 212 loop : -1.99 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 174 TYR 0.010 0.001 TYR B 314 PHE 0.012 0.001 PHE A 366 TRP 0.030 0.001 TRP B 576 HIS 0.006 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.20 (11150) covalent geometry : angle 0.72416 / 0.43 (15133) SS BOND : bond 0.05673 / 2.84 ( 7) SS BOND : angle 9.58703 / 4.10 ( 14) hydrogen bonds : bond 0.15054 / 9.70 ( 580) hydrogen bonds : angle 6.19526 / 4.33 ( 1681) link_NAG-ASN : bond 0.00614 / 0.36 ( 8) link_NAG-ASN : angle 18.69320 / 11.74 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.7955 (m-30) cc_final: 0.7703 (m-30) REVERT: A 209 TYR cc_start: 0.8512 (m-80) cc_final: 0.8253 (m-80) REVERT: A 336 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7208 (mm-30) REVERT: A 352 LYS cc_start: 0.8498 (mttp) cc_final: 0.8214 (mtmt) REVERT: A 358 ASP cc_start: 0.6641 (t70) cc_final: 0.6148 (t70) REVERT: A 536 TRP cc_start: 0.8433 (m100) cc_final: 0.8222 (m100) REVERT: A 734 LEU cc_start: 0.7129 (mp) cc_final: 0.6850 (pt) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.5803 time to fit residues: 119.3945 Evaluate side-chains 133 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.0270 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0020 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.3446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 246 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.120289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.101254 restraints weight = 27367.095| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.62 r_work: 0.3571 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3425 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11165 Z= 0.135 Angle : 0.748 17.798 15171 Z= 0.349 Chirality : 0.053 0.768 1728 Planarity : 0.004 0.039 1879 Dihedral : 5.098 33.824 1496 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.87 % Allowed : 9.96 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.22), residues: 1337 helix: -0.19 (0.19), residues: 700 sheet: -1.39 (0.32), residues: 216 loop : -1.44 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 304 TYR 0.013 0.001 TYR A 776 PHE 0.023 0.001 PHE A 773 TRP 0.018 0.001 TRP B 558 HIS 0.004 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (11150) covalent geometry : angle 0.66645 / 0.33 (15133) SS BOND : bond 0.00304 / 0.17 ( 7) SS BOND : angle 2.05124 / 1.22 ( 14) hydrogen bonds : bond 0.04385 / 2.93 ( 580) hydrogen bonds : angle 4.51609 / 3.24 ( 1681) link_NAG-ASN : bond 0.00956 / 0.46 ( 8) link_NAG-ASN : angle 8.43831 / 5.81 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 TYR cc_start: 0.8639 (m-80) cc_final: 0.8347 (m-80) REVERT: A 255 GLU cc_start: 0.7809 (tt0) cc_final: 0.7466 (tp30) REVERT: A 336 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7488 (mm-30) REVERT: A 352 LYS cc_start: 0.8539 (mttp) cc_final: 0.8304 (mtmt) REVERT: A 358 ASP cc_start: 0.7038 (t70) cc_final: 0.6572 (t70) REVERT: A 456 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7411 (mpp80) REVERT: A 497 ASP cc_start: 0.7919 (p0) cc_final: 0.7634 (p0) REVERT: A 536 TRP cc_start: 0.8448 (m100) cc_final: 0.8229 (m100) REVERT: B 102 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7330 (mtm180) REVERT: B 341 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6196 (mt-10) REVERT: B 511 LEU cc_start: 0.7517 (tp) cc_final: 0.7258 (tt) REVERT: B 608 ASP cc_start: 0.6710 (t70) cc_final: 0.6410 (t70) REVERT: B 630 MET cc_start: 0.7008 (mpp) cc_final: 0.6457 (tmt) outliers start: 22 outliers final: 8 residues processed: 157 average time/residue: 0.5801 time to fit residues: 98.5004 Evaluate side-chains 145 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 657 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 126 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 108 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 122 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 811 ASN B 506 ASN B 698 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.118477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.100036 restraints weight = 19686.745| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.14 r_work: 0.3580 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11165 Z= 0.131 Angle : 0.685 15.310 15171 Z= 0.327 Chirality : 0.048 0.518 1728 Planarity : 0.004 0.043 1879 Dihedral : 4.664 32.093 1496 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.13 % Allowed : 12.68 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.23), residues: 1337 helix: 0.44 (0.20), residues: 700 sheet: -1.06 (0.34), residues: 214 loop : -1.33 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 304 TYR 0.014 0.001 TYR A 776 PHE 0.025 0.001 PHE A 692 TRP 0.016 0.001 TRP B 576 HIS 0.005 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (11150) covalent geometry : angle 0.63203 / 0.31 (15133) SS BOND : bond 0.00316 / 0.17 ( 7) SS BOND : angle 1.81470 / 1.07 ( 14) hydrogen bonds : bond 0.04012 / 2.68 ( 580) hydrogen bonds : angle 4.33355 / 3.09 ( 1681) link_NAG-ASN : bond 0.01082 / 0.53 ( 8) link_NAG-ASN : angle 6.55065 / 4.54 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 TYR cc_start: 0.8569 (m-80) cc_final: 0.8304 (m-80) REVERT: A 336 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7495 (mm-30) REVERT: A 352 LYS cc_start: 0.8420 (mttp) cc_final: 0.8137 (mtmt) REVERT: A 358 ASP cc_start: 0.6963 (t70) cc_final: 0.6491 (t70) REVERT: A 456 ARG cc_start: 0.7643 (mtm-85) cc_final: 0.7410 (mpp80) REVERT: A 536 TRP cc_start: 0.8511 (m100) cc_final: 0.8288 (m100) REVERT: A 776 TYR cc_start: 0.7153 (t80) cc_final: 0.6943 (t80) REVERT: A 779 LEU cc_start: 0.7909 (tm) cc_final: 0.7597 (tt) REVERT: B 102 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7320 (mtm180) REVERT: B 214 ASP cc_start: 0.8154 (t70) cc_final: 0.7900 (t70) REVERT: B 341 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6236 (mt-10) REVERT: B 441 GLU cc_start: 0.7622 (pp20) cc_final: 0.7191 (pp20) REVERT: B 511 LEU cc_start: 0.7509 (tp) cc_final: 0.7263 (tt) REVERT: B 581 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6585 (mp) REVERT: B 615 TRP cc_start: 0.6570 (t60) cc_final: 0.6331 (t-100) REVERT: B 630 MET cc_start: 0.6898 (mpp) cc_final: 0.6389 (tmt) outliers start: 25 outliers final: 13 residues processed: 154 average time/residue: 0.5711 time to fit residues: 95.4910 Evaluate side-chains 148 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 657 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 60 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.117680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.098154 restraints weight = 29236.858| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.72 r_work: 0.3542 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11165 Z= 0.147 Angle : 0.669 14.205 15171 Z= 0.323 Chirality : 0.048 0.457 1728 Planarity : 0.004 0.045 1879 Dihedral : 4.629 31.278 1496 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.72 % Allowed : 14.30 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.23), residues: 1337 helix: 0.69 (0.20), residues: 700 sheet: -0.89 (0.34), residues: 214 loop : -1.29 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 304 TYR 0.009 0.001 TYR B 697 PHE 0.026 0.001 PHE A 773 TRP 0.017 0.001 TRP B 576 HIS 0.005 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (11150) covalent geometry : angle 0.62095 / 0.31 (15133) SS BOND : bond 0.00295 / 0.16 ( 7) SS BOND : angle 1.65391 / 0.98 ( 14) hydrogen bonds : bond 0.04030 / 2.68 ( 580) hydrogen bonds : angle 4.29816 / 3.06 ( 1681) link_NAG-ASN : bond 0.00958 / 0.47 ( 8) link_NAG-ASN : angle 6.14737 / 4.20 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8277 (mt0) cc_final: 0.8074 (mt0) REVERT: A 336 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7630 (mm-30) REVERT: A 352 LYS cc_start: 0.8395 (mttp) cc_final: 0.8159 (mtmt) REVERT: A 358 ASP cc_start: 0.7022 (t70) cc_final: 0.6564 (t70) REVERT: A 494 ARG cc_start: 0.6160 (OUTLIER) cc_final: 0.5844 (pmm150) REVERT: A 536 TRP cc_start: 0.8521 (m100) cc_final: 0.8287 (m100) REVERT: A 776 TYR cc_start: 0.7344 (t80) cc_final: 0.7142 (t80) REVERT: A 803 ARG cc_start: 0.5658 (ptt180) cc_final: 0.5327 (ptt-90) REVERT: B 102 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7426 (mtm180) REVERT: B 214 ASP cc_start: 0.8239 (t70) cc_final: 0.7986 (t70) REVERT: B 341 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6374 (mt-10) REVERT: B 441 GLU cc_start: 0.7716 (pp20) cc_final: 0.7258 (pp20) REVERT: B 501 PHE cc_start: 0.7229 (t80) cc_final: 0.6026 (m-10) REVERT: B 511 LEU cc_start: 0.7624 (tp) cc_final: 0.7402 (tt) REVERT: B 519 MET cc_start: 0.7928 (mmp) cc_final: 0.7723 (mmm) REVERT: B 521 ASN cc_start: 0.7740 (t0) cc_final: 0.7039 (m110) REVERT: B 615 TRP cc_start: 0.6545 (t60) cc_final: 0.6293 (t-100) outliers start: 32 outliers final: 15 residues processed: 158 average time/residue: 0.5722 time to fit residues: 97.7509 Evaluate side-chains 150 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 657 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 69 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 105 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.116272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.096792 restraints weight = 36589.128| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 3.47 r_work: 0.3433 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11165 Z= 0.178 Angle : 0.690 13.595 15171 Z= 0.336 Chirality : 0.049 0.429 1728 Planarity : 0.004 0.046 1879 Dihedral : 4.758 31.703 1496 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.72 % Allowed : 16.34 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.23), residues: 1337 helix: 0.76 (0.20), residues: 698 sheet: -0.77 (0.34), residues: 214 loop : -1.24 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 304 TYR 0.011 0.001 TYR A 209 PHE 0.027 0.001 PHE A 773 TRP 0.019 0.001 TRP B 576 HIS 0.006 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (11150) covalent geometry : angle 0.64692 / 0.33 (15133) SS BOND : bond 0.00695 / 0.37 ( 7) SS BOND : angle 1.94707 / 1.13 ( 14) hydrogen bonds : bond 0.04252 / 2.82 ( 580) hydrogen bonds : angle 4.32816 / 3.09 ( 1681) link_NAG-ASN : bond 0.00920 / 0.45 ( 8) link_NAG-ASN : angle 5.87134 / 3.97 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8318 (mt0) cc_final: 0.8066 (mt0) REVERT: A 336 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7532 (mm-30) REVERT: A 352 LYS cc_start: 0.8546 (mttp) cc_final: 0.8238 (mtmt) REVERT: A 494 ARG cc_start: 0.6300 (OUTLIER) cc_final: 0.5974 (pmm150) REVERT: A 536 TRP cc_start: 0.8550 (m100) cc_final: 0.8339 (m100) REVERT: A 803 ARG cc_start: 0.5679 (ptt180) cc_final: 0.5359 (ptt-90) REVERT: B 102 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7427 (mtm180) REVERT: B 214 ASP cc_start: 0.8233 (t70) cc_final: 0.7975 (t70) REVERT: B 246 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8217 (m-40) REVERT: B 341 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6428 (mt-10) REVERT: B 441 GLU cc_start: 0.7623 (pp20) cc_final: 0.7207 (pp20) REVERT: B 511 LEU cc_start: 0.7608 (tp) cc_final: 0.7383 (tt) outliers start: 32 outliers final: 16 residues processed: 153 average time/residue: 0.5191 time to fit residues: 86.0172 Evaluate side-chains 151 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 581 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 59 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 105 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.117209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.098658 restraints weight = 19640.238| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.10 r_work: 0.3553 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11165 Z= 0.146 Angle : 0.674 13.196 15171 Z= 0.325 Chirality : 0.047 0.401 1728 Planarity : 0.004 0.047 1879 Dihedral : 4.640 30.436 1496 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.81 % Allowed : 17.53 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.23), residues: 1337 helix: 0.89 (0.20), residues: 698 sheet: -0.71 (0.34), residues: 214 loop : -1.18 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.010 0.001 TYR B 314 PHE 0.027 0.001 PHE A 773 TRP 0.013 0.001 TRP B 576 HIS 0.005 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (11150) covalent geometry : angle 0.63314 / 0.32 (15133) SS BOND : bond 0.00331 / 0.18 ( 7) SS BOND : angle 2.03361 / 1.20 ( 14) hydrogen bonds : bond 0.03987 / 2.66 ( 580) hydrogen bonds : angle 4.24980 / 3.03 ( 1681) link_NAG-ASN : bond 0.00947 / 0.46 ( 8) link_NAG-ASN : angle 5.66813 / 3.82 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8299 (mt0) cc_final: 0.8088 (mt0) REVERT: A 325 ASP cc_start: 0.8077 (t0) cc_final: 0.7871 (t70) REVERT: A 336 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7501 (mm-30) REVERT: A 352 LYS cc_start: 0.8538 (mttp) cc_final: 0.8261 (mtmt) REVERT: A 358 ASP cc_start: 0.7020 (t70) cc_final: 0.6518 (t70) REVERT: A 494 ARG cc_start: 0.6284 (OUTLIER) cc_final: 0.5937 (pmm150) REVERT: A 536 TRP cc_start: 0.8521 (m100) cc_final: 0.8314 (m100) REVERT: A 803 ARG cc_start: 0.5651 (ptt180) cc_final: 0.5323 (ptt-90) REVERT: B 102 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7407 (mtm180) REVERT: B 214 ASP cc_start: 0.8235 (t70) cc_final: 0.7967 (t70) REVERT: B 246 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8282 (m-40) REVERT: B 341 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6422 (mt-10) REVERT: B 374 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8124 (pt0) REVERT: B 441 GLU cc_start: 0.7646 (pp20) cc_final: 0.7190 (pp20) REVERT: B 501 PHE cc_start: 0.6716 (t80) cc_final: 0.5664 (m-10) REVERT: B 511 LEU cc_start: 0.7625 (tp) cc_final: 0.7413 (tt) REVERT: B 521 ASN cc_start: 0.7651 (t0) cc_final: 0.7059 (m110) outliers start: 33 outliers final: 18 residues processed: 149 average time/residue: 0.5364 time to fit residues: 86.4875 Evaluate side-chains 152 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 83 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 22 optimal weight: 0.0030 chunk 79 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.118656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.099277 restraints weight = 27463.223| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.57 r_work: 0.3564 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11165 Z= 0.124 Angle : 0.648 12.925 15171 Z= 0.312 Chirality : 0.046 0.375 1728 Planarity : 0.004 0.047 1879 Dihedral : 4.441 28.588 1496 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.38 % Allowed : 18.13 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.24), residues: 1337 helix: 1.07 (0.20), residues: 698 sheet: -0.49 (0.35), residues: 210 loop : -1.14 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 203 TYR 0.019 0.001 TYR A 404 PHE 0.028 0.001 PHE A 773 TRP 0.009 0.001 TRP B 576 HIS 0.003 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (11150) covalent geometry : angle 0.60895 / 0.30 (15133) SS BOND : bond 0.00276 / 0.14 ( 7) SS BOND : angle 1.83951 / 1.09 ( 14) hydrogen bonds : bond 0.03747 / 2.49 ( 580) hydrogen bonds : angle 4.15939 / 2.97 ( 1681) link_NAG-ASN : bond 0.00944 / 0.46 ( 8) link_NAG-ASN : angle 5.42221 / 3.65 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.8544 (mmp80) cc_final: 0.8305 (mmp80) REVERT: A 336 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7517 (mm-30) REVERT: A 352 LYS cc_start: 0.8447 (mttp) cc_final: 0.8178 (mtmt) REVERT: A 358 ASP cc_start: 0.7078 (t70) cc_final: 0.6588 (t70) REVERT: A 444 GLN cc_start: 0.7827 (tp40) cc_final: 0.7429 (tp40) REVERT: A 536 TRP cc_start: 0.8516 (m100) cc_final: 0.8297 (m100) REVERT: A 691 VAL cc_start: 0.8793 (m) cc_final: 0.8530 (p) REVERT: A 803 ARG cc_start: 0.5551 (ptt180) cc_final: 0.5193 (ptt-90) REVERT: B 214 ASP cc_start: 0.8254 (t70) cc_final: 0.7948 (t70) REVERT: B 341 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6451 (mt-10) REVERT: B 374 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8087 (pt0) REVERT: B 441 GLU cc_start: 0.7723 (pp20) cc_final: 0.7223 (pp20) REVERT: B 511 LEU cc_start: 0.7631 (tp) cc_final: 0.7405 (tt) REVERT: B 521 ASN cc_start: 0.7730 (t0) cc_final: 0.7100 (m110) REVERT: B 608 ASP cc_start: 0.6566 (t70) cc_final: 0.6357 (t70) outliers start: 28 outliers final: 18 residues processed: 153 average time/residue: 0.5455 time to fit residues: 90.4936 Evaluate side-chains 150 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 581 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 117 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 0.0040 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 664 GLN B 326 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.116613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.096884 restraints weight = 25847.073| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.53 r_work: 0.3527 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11165 Z= 0.175 Angle : 0.698 13.025 15171 Z= 0.338 Chirality : 0.048 0.378 1728 Planarity : 0.004 0.048 1879 Dihedral : 4.621 29.713 1496 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.64 % Allowed : 18.47 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.24), residues: 1337 helix: 0.99 (0.20), residues: 701 sheet: -0.68 (0.35), residues: 218 loop : -1.10 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 456 TYR 0.018 0.001 TYR A 776 PHE 0.027 0.001 PHE A 773 TRP 0.019 0.001 TRP B 576 HIS 0.006 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.17 (11150) covalent geometry : angle 0.66221 / 0.33 (15133) SS BOND : bond 0.00311 / 0.17 ( 7) SS BOND : angle 1.96746 / 1.15 ( 14) hydrogen bonds : bond 0.04146 / 2.75 ( 580) hydrogen bonds : angle 4.27504 / 3.04 ( 1681) link_NAG-ASN : bond 0.00912 / 0.45 ( 8) link_NAG-ASN : angle 5.43587 / 3.62 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7614 (mm-30) REVERT: A 352 LYS cc_start: 0.8532 (mttp) cc_final: 0.8223 (mtmt) REVERT: A 356 ARG cc_start: 0.7684 (mtm110) cc_final: 0.7476 (mtm110) REVERT: A 415 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7748 (ttm) REVERT: A 444 GLN cc_start: 0.7840 (tp40) cc_final: 0.7430 (tp40) REVERT: A 456 ARG cc_start: 0.7628 (mtm-85) cc_final: 0.7347 (mpp80) REVERT: A 536 TRP cc_start: 0.8536 (m100) cc_final: 0.8301 (m100) REVERT: A 585 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6774 (mtt90) REVERT: A 691 VAL cc_start: 0.8763 (m) cc_final: 0.8506 (p) REVERT: A 730 ILE cc_start: 0.7169 (OUTLIER) cc_final: 0.6895 (mp) REVERT: A 731 VAL cc_start: 0.8160 (t) cc_final: 0.7901 (m) REVERT: A 779 LEU cc_start: 0.7942 (tm) cc_final: 0.7628 (tt) REVERT: A 803 ARG cc_start: 0.5751 (ptt180) cc_final: 0.5428 (ptt-90) REVERT: B 214 ASP cc_start: 0.8274 (t70) cc_final: 0.7966 (t70) REVERT: B 341 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6426 (mt-10) REVERT: B 374 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8085 (pt0) REVERT: B 441 GLU cc_start: 0.7747 (pp20) cc_final: 0.7252 (pp20) REVERT: B 511 LEU cc_start: 0.7661 (tp) cc_final: 0.7457 (tt) REVERT: B 519 MET cc_start: 0.7760 (mmp) cc_final: 0.7557 (mmm) REVERT: B 521 ASN cc_start: 0.7741 (t0) cc_final: 0.7074 (m110) REVERT: B 608 ASP cc_start: 0.6702 (t70) cc_final: 0.6424 (t70) outliers start: 31 outliers final: 20 residues processed: 152 average time/residue: 0.5336 time to fit residues: 87.9237 Evaluate side-chains 156 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 581 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 68 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 29 optimal weight: 0.0270 chunk 34 optimal weight: 0.0170 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 128 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.119344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.099929 restraints weight = 27458.216| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.61 r_work: 0.3579 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11165 Z= 0.116 Angle : 0.658 12.713 15171 Z= 0.317 Chirality : 0.045 0.354 1728 Planarity : 0.004 0.048 1879 Dihedral : 4.400 27.968 1496 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.70 % Allowed : 19.57 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.24), residues: 1337 helix: 1.17 (0.20), residues: 701 sheet: -0.35 (0.37), residues: 201 loop : -1.08 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 456 TYR 0.022 0.001 TYR A 776 PHE 0.029 0.001 PHE A 773 TRP 0.011 0.001 TRP A 687 HIS 0.002 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (11150) covalent geometry : angle 0.62157 / 0.31 (15133) SS BOND : bond 0.00499 / 0.26 ( 7) SS BOND : angle 2.02838 / 1.13 ( 14) hydrogen bonds : bond 0.03618 / 2.40 ( 580) hydrogen bonds : angle 4.10381 / 2.93 ( 1681) link_NAG-ASN : bond 0.00968 / 0.47 ( 8) link_NAG-ASN : angle 5.22495 / 3.51 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7544 (mm-30) REVERT: A 352 LYS cc_start: 0.8434 (mttp) cc_final: 0.8150 (mtmt) REVERT: A 356 ARG cc_start: 0.7625 (mtm110) cc_final: 0.7412 (mtm110) REVERT: A 358 ASP cc_start: 0.6986 (t70) cc_final: 0.6501 (t70) REVERT: A 444 GLN cc_start: 0.7778 (tp40) cc_final: 0.7374 (tp40) REVERT: A 456 ARG cc_start: 0.7613 (mtm-85) cc_final: 0.7325 (mpp80) REVERT: A 536 TRP cc_start: 0.8518 (m100) cc_final: 0.8302 (m100) REVERT: A 730 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6892 (mp) REVERT: A 779 LEU cc_start: 0.7953 (tm) cc_final: 0.7636 (tt) REVERT: A 803 ARG cc_start: 0.5505 (ptt180) cc_final: 0.5156 (ptt-90) REVERT: B 129 MET cc_start: 0.8897 (mtt) cc_final: 0.8517 (mtt) REVERT: B 214 ASP cc_start: 0.8257 (t70) cc_final: 0.7943 (t70) REVERT: B 341 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6392 (mt-10) REVERT: B 374 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8083 (pt0) REVERT: B 441 GLU cc_start: 0.7716 (pp20) cc_final: 0.7216 (pp20) REVERT: B 511 LEU cc_start: 0.7631 (tp) cc_final: 0.7418 (tt) REVERT: B 521 ASN cc_start: 0.7717 (t0) cc_final: 0.7082 (m110) REVERT: B 608 ASP cc_start: 0.6557 (t70) cc_final: 0.6278 (t70) outliers start: 20 outliers final: 13 residues processed: 143 average time/residue: 0.5056 time to fit residues: 78.7254 Evaluate side-chains 143 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 581 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 92 optimal weight: 0.0010 chunk 20 optimal weight: 0.0070 chunk 88 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.5406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.119262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.100288 restraints weight = 31010.255| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.79 r_work: 0.3538 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11165 Z= 0.133 Angle : 0.671 12.686 15171 Z= 0.323 Chirality : 0.046 0.353 1728 Planarity : 0.004 0.047 1879 Dihedral : 4.430 28.948 1496 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.53 % Allowed : 20.09 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.24), residues: 1337 helix: 1.22 (0.20), residues: 701 sheet: -0.44 (0.36), residues: 214 loop : -1.07 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 456 TYR 0.022 0.001 TYR A 776 PHE 0.028 0.001 PHE A 773 TRP 0.012 0.001 TRP B 576 HIS 0.003 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (11150) covalent geometry : angle 0.63679 / 0.32 (15133) SS BOND : bond 0.00301 / 0.16 ( 7) SS BOND : angle 1.85522 / 1.09 ( 14) hydrogen bonds : bond 0.03746 / 2.48 ( 580) hydrogen bonds : angle 4.11998 / 2.94 ( 1681) link_NAG-ASN : bond 0.00948 / 0.46 ( 8) link_NAG-ASN : angle 5.18197 / 3.46 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 336 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7400 (mm-30) REVERT: A 352 LYS cc_start: 0.8455 (mttp) cc_final: 0.8154 (mtmt) REVERT: A 356 ARG cc_start: 0.7540 (mtm110) cc_final: 0.7311 (mtm110) REVERT: A 358 ASP cc_start: 0.6911 (t70) cc_final: 0.6419 (t70) REVERT: A 444 GLN cc_start: 0.7791 (tp40) cc_final: 0.7369 (tp40) REVERT: A 456 ARG cc_start: 0.7674 (mtm-85) cc_final: 0.7422 (mpp80) REVERT: A 536 TRP cc_start: 0.8479 (m100) cc_final: 0.8267 (m100) REVERT: A 779 LEU cc_start: 0.7972 (tm) cc_final: 0.7624 (tt) REVERT: A 803 ARG cc_start: 0.5385 (ptt180) cc_final: 0.5031 (ptt-90) REVERT: B 129 MET cc_start: 0.8745 (mtt) cc_final: 0.8346 (mtt) REVERT: B 214 ASP cc_start: 0.8149 (t70) cc_final: 0.7877 (t70) REVERT: B 341 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6279 (mt-10) REVERT: B 374 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8093 (pt0) REVERT: B 441 GLU cc_start: 0.7459 (pp20) cc_final: 0.6987 (pp20) REVERT: B 521 ASN cc_start: 0.7505 (t0) cc_final: 0.6997 (m110) REVERT: B 608 ASP cc_start: 0.6431 (t70) cc_final: 0.6225 (t70) outliers start: 18 outliers final: 14 residues processed: 136 average time/residue: 0.5552 time to fit residues: 81.6960 Evaluate side-chains 139 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 581 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 61 optimal weight: 0.0040 chunk 22 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.117415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.097531 restraints weight = 40414.996| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 3.83 r_work: 0.3459 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11165 Z= 0.171 Angle : 0.706 12.736 15171 Z= 0.341 Chirality : 0.048 0.361 1728 Planarity : 0.004 0.051 1879 Dihedral : 4.606 30.146 1496 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.79 % Allowed : 20.00 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.24), residues: 1337 helix: 1.13 (0.20), residues: 700 sheet: -0.48 (0.36), residues: 214 loop : -1.05 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 456 TYR 0.021 0.001 TYR A 776 PHE 0.028 0.001 PHE A 773 TRP 0.018 0.001 TRP B 576 HIS 0.006 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (11150) covalent geometry : angle 0.67270 / 0.33 (15133) SS BOND : bond 0.00307 / 0.16 ( 7) SS BOND : angle 1.99614 / 1.18 ( 14) hydrogen bonds : bond 0.04069 / 2.69 ( 580) hydrogen bonds : angle 4.22578 / 3.01 ( 1681) link_NAG-ASN : bond 0.00921 / 0.45 ( 8) link_NAG-ASN : angle 5.19892 / 3.45 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4129.96 seconds wall clock time: 71 minutes 4.56 seconds (4264.56 seconds total)